VIRMA

vir like m6A methyltransferase associated, the group of Armadillo like helical domain containing|m6A methyltransferase complex|WTAP complex

Basic information

Region (hg38): 8:94487688-94553529

Previous symbols: [ "KIAA1429" ]

Links

ENSG00000164944 ∙ NCBI:25962 ∙ OMIM:616447 ∙ HGNC:24500 ∙ Uniprot:Q69YN4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VIRMA gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIRMA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in VIRMA

This is a list of pathogenic ClinVar variants found in the VIRMA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-94488843-G-A		not specified	Uncertain significance (Dec 03, 2021)
8-94488854-C-T		not specified	Uncertain significance (Sep 17, 2021)
8-94489963-G-A		not specified	Uncertain significance (Mar 01, 2023)
8-94490029-T-C		not specified	Uncertain significance (Jun 30, 2022)
8-94491586-G-A		not specified	Uncertain significance (Jun 05, 2023)
8-94491593-G-A		not specified	Uncertain significance (Oct 10, 2023)
8-94491692-G-A		not specified	Uncertain significance (Aug 08, 2023)
8-94492678-G-T		not specified	Uncertain significance (Mar 20, 2023)
8-94492798-T-G		not specified	Uncertain significance (Apr 13, 2023)
8-94494948-T-A		not specified	Uncertain significance (Mar 07, 2024)
8-94494948-T-C		not specified	Uncertain significance (May 11, 2022)
8-94495791-T-A		not specified	Uncertain significance (May 11, 2022)
8-94495794-C-T		not specified	Uncertain significance (Dec 17, 2023)
8-94495852-C-T		not specified	Uncertain significance (Mar 01, 2024)
8-94496423-T-C		not specified	Uncertain significance (Aug 02, 2022)
8-94496464-T-G		not specified	Uncertain significance (Jan 03, 2024)
8-94496475-G-C		not specified	Uncertain significance (Aug 30, 2021)
8-94499376-T-C			Uncertain significance (May 01, 2022)
8-94499432-C-A		not specified	Uncertain significance (Dec 15, 2023)
8-94506599-G-A		not specified	Uncertain significance (Dec 27, 2023)
8-94509720-C-T		not specified	Likely benign (Dec 13, 2022)
8-94509753-C-T		not specified	Uncertain significance (Feb 06, 2023)
8-94509764-C-T		not specified	Uncertain significance (Nov 17, 2023)
8-94509831-T-G		not specified	Uncertain significance (Nov 20, 2023)
8-94510472-T-A		not specified	Uncertain significance (Apr 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VIRMA	protein_coding	protein_coding	ENST00000297591	24	65837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00562	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.77	706	946	0.746	0.0000480	11827
Missense in Polyphen		224	402.26	0.55686		4905
Synonymous	-0.313	335	328	1.02	0.0000157	3522
Loss of Function	6.83	15	81.5	0.184	0.00000448	1043

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000427	0.000424
Ashkenazi Jewish	0.000220	0.000198
East Asian	0.00	0.00
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000214	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000131	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:24981863, PubMed:29507755). Acts as a key regulator of m6A methylation by promoting m6A methylation of mRNAs in the 3'-UTR near the stop codon: recruits the catalytic core components METTL3 and METTL14, thereby guiding m6A methylation at specific sites (PubMed:29507755). Required for mRNA polyadenylation via its role in selective m6A methylation: m6A methylation of mRNAs in the 3'-UTR near the stop codon correlating with alternative polyadenylation (APA) (PubMed:29507755). {ECO:0000269|PubMed:24981863, ECO:0000269|PubMed:29507755}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.52

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.575
• ghis: 0.623

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Virma
• Phenotype: skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: mRNA processing;multicellular organism development;RNA splicing;mRNA methylation;mRNA alternative polyadenylation
• Cellular component: nucleoplasm;cytosol;nuclear body;nuclear speck;RNA N6-methyladenosine methyltransferase complex
• Molecular function: RNA binding;protein binding